Discover ga4gh/large-scale-genomics-wiki Open Source project

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

214

benchmarking-tools

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

188

ga4gh-server

The WES API is a standard way to run and manage portable workflows.

workflow-execution-service-schemas

task-execution-schemas

vrs

Extensible specification for representing and uniquely identifying biological sequence variation

A repository for the schemas used for the Data Repository Service.

data-repository-service-schemas

vrs-python

GA4GH Variation Representation Python Implementation

Documentation for the MatchmakerExchange APIs

mme-apis

APIs for discovering genomics tools, their metadata and their containers

tool-registry-service-schemas

Shell

data-security

This is the repository for the GA4GH Data Security Work Stream, containing AAI and DSIP.

An information model for representing variant annotations.

va-spec

Python client for GA4GH htsget protocol

htsget

a place for GA4GH-related wiki pages

wiki

refget

GA4GH Refget specifications docs

Home for the GA4GH Quality Control of Whole Genome Sequencing metrics and reference implementations

quality-control-wgs

Repository for the family history/pedigree project

pedigree

fasp-scripts

Reference server implementation for the GA4GH HTSget API standard.

htsget-refserver

task-execution-server

compliance

Compliance test suite for the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Interoperable execution of workflows using GA4GH APIs

metadata-team

cloud-interop-testing

TASC aids the harmonisation of aspects of GA4GH's various products that would otherwise prevent different products from being used together conveniently.

TASC

gh-openapi-docs

Package for building OpenAPI schema docs and UI for gh-pages

Repository for the Google Summer of Code for the Reference Retrieval API

refget-compliance-suite

Retrieve omics data and metadata from DRS-compliant web services

ga4gh-drs-client

Client implementation for accessing GA4GH APIs

ga4gh-client

ISMB 2022 tutorial on FASP and Starter Kit

human-pangenome-project

Human Pangenome Project

Get-Started-with-GA4GH-APIs

Implementation registry service for cataloguing implementations of GA4GH standards

ga4gh-registry

pedigree_family_history_terminology

Starter Kit server implementation of the GA4GH Workflow Execution Service (WES) specification

ga4gh-starter-kit-wes

Sample code to inform a discussion around content-addressable storage

gastore

Scala

tool-registry-validator

Used to validate APIs that implement https://github.com/ga4gh/tool-registry-schemas

Open, extensible server implementation of the GA4GH Data Repository Service (DRS) specification

ga4gh-starter-kit-drs

GA4GH Data Working Group website hosted at ga4gh.org

dwg-website

Repository for the GA4GH Future of VCF team.

future-of-vcf

g2p-team

GitHub Repo for the Genotype to Phenotype Task Team

ga4gh-common

common modules for GA4GH schemas, client and server, collected into one package

GA4GH Software Security Implementation Guide

ADA-M

tool-registry-reference-implementation

Clojure

swg-ssig

fasp-clients

a place for client code from the FASP effort

Repository to track DWG hackathon 2016 projects

duri

hackathon2016

ga4gh-consent-policy

ga4gh-testbed-ui

Web UI for the GA4GH Testbed Reporting service

C-based library for manipulating HGVS-formatted variants

hgvs-lib

approval-tracker

GitHub repository for tracking the progress of specification approval

refget-cloud

AWS serverless implementation of the refget service

Starter Kit server implementation of the GA4GH Data Connect specification

ga4gh-starter-kit-data-connect

Schedule the processing of ENA sequences and upload to S3 public dataset

refget-loader

Common classes and schemas used by all GKS specifications (ie. VR, VA, etc..)

gks-common

Makefile

data-object-service-schemas

Intermediate repo to manage redirects to DRS repository (original home for DOS)

workflow-execution-server

pedigree-tools

A hub for working on the GA4GH Reference Server, Schemas, and Compliance projects.

Strategic-Refresh

build

Shell

ga4gh-crypt4gh

htsget-compliance

Compliance testing for htsget deployments

Project tracking for GA4GH Variation Representation Specification hackathons

vrs-hackathons

GA4GH-wide testbed infrastructure for hosting testbed reports

experiments-metadata

ga4gh-testbed-api

Best practices (spec development, project/issue management, testing, CI, etc.) across all Cloud Work Stream standards

compliance-tests-ga4gh-tes

compliance-tests-ga4gh-wes

cloud-best-practices

cloud-interop-ui

Manage Cloud interoperability test plugins and schedules through web interface

Common utils library for GA4GH Starter Kit web services

ga4gh-starter-kit-common

Test suites to validate implementations of GA4GH Cloud APIs

product-process

tool-registry-server

cloud-conformance-testing

ga4gh-testbed-lib

Python library for creating GA4GH testbed reports according to a harmonized, cross-workstream schema

Project tracking for GA4GH Computable Cohort Representation Hackathons

cohort-rep-hackathon

Central UI server connecting to other Passport-related microservices (ory hydra, ory kratos)

ga4gh-starter-kit-passport-ui

TypeScript

gks-starter-repo

A starting point to copy and use for teams wishing to quickly define their own schema extensions and profiles to the VA, Cat-VRS or VRS schemas.